phyloframe 0.1.0__tar.gz

phyloframe-0.1.0/.editorconfig

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+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[Makefile]
+indent_style = tab

phyloframe-0.1.0/.github/ISSUE_TEMPLATE.md

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+* phyloframe version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

phyloframe-0.1.0/.github/workflows/ci.yaml

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+name: ci
+
+on:
+  push:
+    branches:
+    - master
+    tags:
+      - '*'
+  pull_request:
+    branches:
+    - '*'
+  schedule:
+    - cron: '0 0 * * 1'  # weekly
+  workflow_dispatch:
+jobs:
+  test:
+    runs-on: ubuntu-24.04
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        subdivision:
+          - "test_legacy"
+          - "test_auxlib"
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip install tox tox-gh-actions
+    - name: Test with tox
+      run: |
+        export PHYLOFRAME_TESTS_SUBDIVISION=${{ matrix.subdivision }}
+        tox
+
+  cli-smoke:
+    runs-on: ubuntu-24.04
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.10"
+    - name: Install Python dependencies
+      uses: py-actions/py-dependency-install@v4
+      with:
+        path: "requirements-dev/requirements-testing.txt"
+    - name: Run examples
+      run: |
+        python3 -m phyloframe
+        python3 -m phyloframe.legacy._alifestd_as_newick_asexual --help
+        python3 -m phyloframe.legacy._alifestd_downsample_tips_asexual --help
+        python3 -m phyloframe.legacy._alifestd_try_add_ancestor_list_col --help
+
+  coverage:
+    runs-on: ubuntu-24.04
+    strategy:
+      fail-fast: false
+      matrix:
+        subdivision:
+          - "test_legacy"
+          - "test_auxlib"
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.12"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        python -m pip install -r requirements-dev/py312/requirements-testing.txt
+    - name: Log coverage configuration
+      run: coverage debug sys
+    - name: Run tests with coverage report
+      run: coverage run -m pytest tests/test_phyloframe/${{ matrix.subdivision }}
+    - uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        flags: tests
+        fail_ci_if_error: true
+        verbose: true
+
+  tidy:
+    runs-on: ubuntu-24.04
+    steps:
+    - name: Install apt dependencies
+      run: sudo apt-get install -y rename
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        python -m pip install -r requirements-dev/py310/requirements-testing.txt
+    - name: Test isort tidyness
+      uses: jamescurtin/isort-action@master
+      with:
+          requirementsFiles: "requirements-dev/py310/requirements-testing.txt"
+    - name: Test Black tidyness
+      uses: psf/black@27d20144a7517594e24a1649451177b2a11284be
+      with:
+          version: "22.10.0"
+    - uses: editorconfig-checker/action-editorconfig-checker@main
+    - name: Test editorconfig tidyness
+      run: editorconfig-checker
+    - name: Test tidy/ tidyness
+      run: ./tidy/test_tidy.sh
+
+  packaging-bdist:
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build bdist
+        run: |
+          python3 -m venv env
+          source env/bin/activate
+          python3 -m pip install -r requirements-dev/requirements-release.txt
+          python3 setup.py bdist_wheel
+          tree dist
+          deactivate
+      - name: Upgrade pip
+        run: python3 -m pip install pip --upgrade
+      - name: Install from bdist
+        run: python3 -m pip install dist/*.whl
+      - name: Test install
+        run: |
+          find . -type f -name '*.py' -exec rm {} \;
+          find . -type f -name '*.pyi' -exec rm {} \;
+          python3 -c "import phyloframe; print(phyloframe.__version__)"
+
+  packaging-sdist:
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build sdist
+        run: |
+          python3 -m venv env
+          source env/bin/activate
+          python3 -m pip install -r requirements-dev/requirements-release.txt
+          python3 setup.py sdist
+          tree dist
+          deactivate
+      - name: Upgrade pip
+        run: python3 -m pip install pip --upgrade
+      - name: Install from sdist
+        run: python3 -m pip install dist/*.tar.gz
+      - name: Test install
+        run: |
+          find . -type f -name '*.py' -exec rm {} \;
+          find . -type f -name '*.pyi' -exec rm {} \;
+          python3 -c "import phyloframe; print(phyloframe.__version__)"
+
+  packaging-source:
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Upgrade pip
+        run: python3 -m pip install pip --upgrade
+      - name: Install from source
+        run: python3 -m pip install .
+      - name: Test install
+        run: |
+          rm -rf *
+          cd
+          python3 -c "import phyloframe; print(phyloframe.__version__)"
+
+  deploy-ghcr:
+    name: Docker Image Deploy
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Set Tags
+        id: set_tags
+        run: |
+          if [[ "${GITHUB_REF_NAME}" != *merge ]]; then
+            echo "TAGS=ghcr.io/mmore500/phyloframe:latest,ghcr.io/mmore500/phyloframe:${GITHUB_REF_NAME}" >> $GITHUB_ENV
+          else
+            echo "TAGS=ghcr.io/mmore500/phyloframe:latest" >> $GITHUB_ENV
+          fi
+      - name: Build and Push to GitHub Container Registry
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: ${{ github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/v') }}
+          tags: ${{ env.TAGS }}
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  deploy-test:
+    runs-on: ubuntu-24.04
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install -r requirements-dev/py310/requirements-release.txt
+    - name: Build package
+      run: python setup.py egg_info --tag-build=".post${{github.run_number}}" sdist bdist_wheel
+    - name: Test publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository-url: https://test.pypi.org/legacy/
+        verbose: true
+    - name: Install from test PyPI
+      run: |
+        rm -rf *
+        python3 -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ phyloframe
+    - name: Test install
+      run: |
+        python3 -c "import phyloframe; print(phyloframe.__version__)"
+
+  deploy:
+    if: startsWith(github.ref, 'refs/tags/v')
+    needs:
+      - build_sdist
+      - coverage
+      - cli-smoke
+      - deploy-test
+      - packaging-bdist
+      - packaging-sdist
+      - packaging-source
+      - test
+      - tidy
+    runs-on: ubuntu-24.04
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        python -m pip install -r requirements-dev/py310/requirements-release.txt
+    - uses: actions/download-artifact@v4
+      with:
+        pattern: cibw-*
+        path: dist
+        merge-multiple: true
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}
+        verbose: true

phyloframe-0.1.0/.gitignore

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+# documentation
+docs/_autosummary/
+docs/api
+docs/_modules
+docs/_build
+docs/readme.rst
+docs/citing.rst
+docs/projects.rst
+docs/publications.rst
+docs/index.rst
+
+joss/paper.pdf
+
+# test output
+teeplots/
+
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintainted in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# End of https://www.toptal.com/developers/gitignore/api/python
+
+# Compiled Object files
+**/.DS_Store
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+**/cmake-build-debug
+**/CMakeCache.txt
+**/cmake_install.cmake
+**/install_manifest.txt
+**/CMakeFiles/
+**/CTestTestfile.cmake
+**/Makefile
+**/*.cbp
+**/CMakeScripts
+**/compile_commands.json
+
+include/divisible/*
+
+
+## Local
+
+.idea/*.xml
+
+build/**/*
+
+include/*
+lib/*
+bin/*
+test/test_runner
+
+**/.rendered*.cpp

phyloframe-0.1.0/.readthedocs.yaml

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+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  apt_packages:
+    - pandoc
+  tools:
+    python: "3.11"
+  commands:
+    - pip install -r requirements-dev/requirements-docs.txt
+    - pip install . --no-deps
+    - make -C docs/ html
+    - mkdir -p _readthedocs
+    - rm -rf _readthedocs/html
+    - cp -r docs/_build/html _readthedocs/

phyloframe-0.1.0/AUTHORS.rst

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+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Matthew Andres Moreno <m.more500@gmail.com>
+
+Contributors
+------------
+
+* Connor Yang
+* Santiago Rodriguez-Papa
+* Vivaan Singhvi

phyloframe-0.1.0/CITATION.cff

@@ -0,0 +1,9 @@
+cff-version: 0.1.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Moreno
+    given-names: Matthew Andres
+    orcid: https://orcid.org/0000-0003-4726-4479
+title: "phyloframe"
+version: 0.1.0
+url: "https://github.com/mmore500/phyloframe"